1. Insert a Synth:
   
2. Disconnect the Synth. Input is still correctly associated:
   
3. Undo Insert Synth (Ctrl+Z)
4. Redo (Ctrl+Shift+Z)
5. Input reference is missing:
   

NOTE: This also occurs when you "Delete Synth" and Redo, when the Syth is disconnected.

I don't understand why you want to "disconnect" the input? All audio tracks have an input field, but the TTS-1 doesn't accept audio inputs so there is no reason to "disconnect" it. Unless I'm missing something, I think you're saying that if you do something irrelevant, it produces an irrelevant result.
 
Also with both split or simple instrument tracks, I can insert, change the MIDI input assignment to whatever, undo the insert, redo, and everything comes back the way it was. So I'm not sure what the problem is there, either.
 
I need to understand what you're trying to accomplish, and how whatever you're describing prevents you from doing it, before I can offer any suggestions for a fix. Also exact steps to reproduce would be helpful because if I do what I think you're trying to do, it works as expected.

I have a complete symphony orchestra template, with 23 instances of Kontakt (flutes, oboes, horns, etc).
Leaving all instances connected will consumes a large amount of RAM, as well as consuming a huge amount of time to load them.
As I do not always use all the instruments, I leave the synths disconnected, connecting only as I need them.
Also, since Sonar does not have a way to reorder the synths in Synth Rack, I use this technique to reorder them, thus keeping everything in order.
The problem then is that I can not delete a synth and undo the operation, since this will lose the input references.
I hope this has explained the reasons.
As much as it is an unusual situation, this is still a bug, which does not occur in earlier versions.
I hope bakers can solve this soon.
 

Okay, that's unusual but I can see why you want to do it. I don't know if it happening in previous versions and not in this one is a bug, or caused by the Duplicate Track function.
 
As a solution, can you just Archive the instrument tracks you don't want to use at any given moment, then unarchive when you want to use them? I believe that disconnects from the CPU, but I don't know about RAM.